Barker’s CFL coaching career began in 1996 as a member of the Montreal Alouettes coaching staff. The Alouettes set a team record for wins, but lost in the Eastern Division Finals to the Toronto Argonauts. In 1997, he was named the Argonauts’ Co-Offensive Coordinator and Offensive Line Coach and was instrumental in guiding one of the best offences in CFL history. In 1999 he replaced the departing Don Matthews as head coach of the Argonauts, becoming the youngest head coach in the CFL.

On February 9, 2010, Barker returned to the Toronto Argonauts for his second stint as their head coach. After leading the Argos to the playoffs for the first time since 2007, Barker assumed the role of general manager on December 15, 2010, replacing Adam Rita whose contract was not renewed.

The CFL announced on February 25, 2011 that Barker was the Coach of the Year for 2010, winning the Annis Stukus Trophy.